/* 
 * GeneID validating plugin for BAT.
 * Copyright (C) 2006 Bob Zimmermann <rpz@cse.wustl.edu>
 *
 *  This file is a part of BAT.
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 * BAT_GeneID_Validator.h
 *
 * Validates the gene id of the bats by merging similar bats.
 *
 * $Id: BAT_GeneID_Validator.h 1407 2006-09-20 20:28:22Z rpz $
 *
 */

#ifndef BAT_GENEID_VALIDATOR_H
#  define BAT_GENEID_VALIDATOR_H

#  include "BAT_Annotation.h"
#  include "BAT_Validator.h"
#include "partition.h"

extern BAT_Validate_Plugin BAT_GeneID_Validate_Plugin;
typedef struct _BAT_GeneID_Validate_Context BAT_GeneID_Validate_Context;
typedef struct _BAT_GeneID_Validate_Transcript_Status
  BAT_GeneID_Validate_Transcript_Status;
typedef struct _BAT_GeneID_Validate_Mapped_Feature
  BAT_GeneID_Validate_Mapped_Feature;

struct _BAT_GeneID_Validate_Context
{
  int enabled;
  int match_all_features;
  int dont_delete;
};

void *BAT_GeneID_Validator_new ();
void BAT_GeneID_Validator_delete (void *, int);
int BAT_GeneID_Validator_cmd_parse (void *, int, char **);
BAT_GeneTab *BAT_GeneID_Validator_validate_gene_table (void *, BAT_GeneTab *);

#endif /* BAT_GENEID_VALIDATOR_H */
